Hi Bruce, et al,
The Markov random field approach with FSL FAST is intensive (~ 2000 sec on Athlon 1700, 1Gb PC2700 on VIA KT333A) and the results "appear" to be good. Of course, it could be better to measure the quantity on the scanner. Would this approach require access and modification of the kspace images before reconstruction? Naturally we could all rest easily if the scanner engineering and signal processing took care of the problem ;-) We don't have a research scanner and any access to any of that :-( It would be nice to evaluate this latter "physical" solution with that from FAST. Thanks for clarifying the mri_normalize process. It will be interesting, although overkill, to see what happens when FreeSurfer is fed one of the volumes after RF correction with FAST. In particular, whether it will improve the segmentation any. Another interesting experiment might be to segment the WM with freesurfer and use that volume as a prior input to FAST. Again, overkill, but anything that could improve the automation of the first segmentation stage might decrease the latter manual editing. The cost is the extra processing overheads. Yes, there is some other work to be done on just the RF bias corrected volume. Cheers, Darren ----- Original Message ----- From: "Bruce Fischl" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Thursday, August 29, 2002 9:30 PM Subject: Re: RF bias correction with mri_convert > p.s. what we do is not really bias field estimation/correction, but > something much more aggressive, really a pre-segmentation, which accounts > for bias fields as well as tissue inhomogeneity. If what you want is really > the bias field for some other purpose, you're probably better of using the > EM stuff from the FSL (unless you can measure it directly with your > scanner, which is the best solution!). > > Bruce > > On Thu, 29 Aug 2002, Stephen Smith wrote: > > > > > Hi - no, it doesn't - that is part of the initial freesurfer processing > > (which estimates white matter and then estimates bias field on the basis > > of white matter points), not the format conversion. > > > > ttfn, Steve. > > > > On Thu, 29 Aug 2002, Darren Weber wrote: > > > > > > > > Dear Bruce et al, > > > > > > does mri_convert automatically apply RF bias field estimation/correction? > > > If it can do the RF bias correction, what is the best command line option > > > for this? > > > > > > Take care, Darren > > > > > > > > > -- > > > Darren Weber, PhD Student > > > Cognitive Neuroscience, School of Psychology > > > Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust. > > > Ph: (61 8) 8201 3889, Fax: (61 8) 8201 3877 > > > http://203.3.164.46/~dlw/homepages/index.html > > > > > > > > > > > > > Stephen M. Smith > > Head of Image Analysis, FMRIB > > > > Oxford University Centre for Functional MRI of the Brain > > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > > +44 (0) 1865 222726 (fax 222717) > > > > [EMAIL PROTECTED] http://www.fmrib.ox.ac.uk/~steve > > > >
